Starting phenix.real_space_refine on Mon Mar 11 21:45:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/03_2024/7rgq_24454_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/03_2024/7rgq_24454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/03_2024/7rgq_24454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/03_2024/7rgq_24454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/03_2024/7rgq_24454_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/03_2024/7rgq_24454_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.500 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 96 5.49 5 S 184 5.16 5 C 18840 2.51 5 N 5160 2.21 5 O 6008 1.98 5 H 29544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 162": "OD1" <-> "OD2" Residue "D ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 162": "OD1" <-> "OD2" Residue "E ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E ASP 216": "OD1" <-> "OD2" Residue "E ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 162": "OD1" <-> "OD2" Residue "F ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F ASP 274": "OD1" <-> "OD2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 162": "OD1" <-> "OD2" Residue "G ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 214": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 254": "OE1" <-> "OE2" Residue "G TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G ASP 274": "OD1" <-> "OD2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 162": "OD1" <-> "OD2" Residue "H ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 214": "OD1" <-> "OD2" Residue "H ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 239": "OD1" <-> "OD2" Residue "H ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 274": "OD1" <-> "OD2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 59832 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "B" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "C" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "D" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "E" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "F" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "G" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "H" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 19.51, per 1000 atoms: 0.33 Number of scatterers: 59832 At special positions: 0 Unit cell: (151.96, 151.96, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 184 16.00 P 96 15.00 O 6008 8.00 N 5160 7.00 C 18840 6.00 H 29544 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.14 Conformation dependent library (CDL) restraints added in 4.9 seconds 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 147 helices and 53 sheets defined 34.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 4.160A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 4.227A pdb=" N MET A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 removed outlier: 4.158A pdb=" N PHE A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.987A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.845A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.591A pdb=" N TYR A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix removed outlier: 3.602A pdb=" N HIS A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 470 " --> pdb=" O HIS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'B' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 76 through 85 removed outlier: 4.227A pdb=" N MET B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 removed outlier: 4.214A pdb=" N PHE B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 254 through 265 removed outlier: 4.000A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.961A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.590A pdb=" N TYR B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix removed outlier: 3.550A pdb=" N HIS B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 470 " --> pdb=" O HIS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'C' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 76 through 85 removed outlier: 4.091A pdb=" N MET C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 110 removed outlier: 4.242A pdb=" N PHE C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 196 through 202 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 256 through 265 removed outlier: 4.234A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 4.970A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 354 removed outlier: 3.590A pdb=" N TYR C 348 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix removed outlier: 3.552A pdb=" N HIS C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP C 470 " --> pdb=" O HIS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'D' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 76 through 85 removed outlier: 4.227A pdb=" N MET D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 110 removed outlier: 4.192A pdb=" N PHE D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 137 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 196 through 203 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.923A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 263 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.838A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.591A pdb=" N TYR D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix removed outlier: 3.937A pdb=" N ASP D 470 " --> pdb=" O HIS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'E' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 76 through 85 removed outlier: 4.227A pdb=" N MET E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 removed outlier: 4.223A pdb=" N PHE E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 196 through 203 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 256 through 265 removed outlier: 4.250A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 4.917A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 3.590A pdb=" N TYR E 348 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix removed outlier: 3.607A pdb=" N HIS E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP E 470 " --> pdb=" O HIS E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'F' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 76 through 85 removed outlier: 4.226A pdb=" N MET F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 110 removed outlier: 4.248A pdb=" N PHE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 196 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.600A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 263 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 4.968A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.590A pdb=" N TYR F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix removed outlier: 3.562A pdb=" N HIS F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP F 470 " --> pdb=" O HIS F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'G' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 76 through 85 removed outlier: 4.226A pdb=" N MET G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 110 removed outlier: 4.334A pdb=" N PHE G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 194 through 203 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 254 through 265 removed outlier: 3.569A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 263 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 265 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 4.996A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 354 removed outlier: 3.591A pdb=" N TYR G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 414 through 416 No H-bonds generated for 'chain 'G' and resid 414 through 416' Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix removed outlier: 3.537A pdb=" N HIS G 466 " --> pdb=" O ALA G 462 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G 467 " --> pdb=" O GLY G 463 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP G 470 " --> pdb=" O HIS G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 498 No H-bonds generated for 'chain 'G' and resid 495 through 498' Processing helix chain 'H' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 76 through 85 removed outlier: 4.226A pdb=" N MET H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 110 removed outlier: 4.219A pdb=" N PHE H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 196 through 203 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 254 through 265 removed outlier: 3.959A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 263 " --> pdb=" O LEU H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 4.976A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 3.591A pdb=" N TYR H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 414 through 416 No H-bonds generated for 'chain 'H' and resid 414 through 416' Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix removed outlier: 3.535A pdb=" N HIS H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP H 470 " --> pdb=" O HIS H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 497 No H-bonds generated for 'chain 'H' and resid 495 through 497' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.300A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 383 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 189 removed outlier: 3.574A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.752A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 408 through 412 Processing sheet with id= F, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.817A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= H, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= I, first strand: chain 'B' and resid 187 through 189 removed outlier: 8.191A pdb=" N ALA B 188 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.762A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 320 through 323 removed outlier: 7.824A pdb=" N VAL B 323 " --> pdb=" O PRO B 360 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 362 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR B 383 " --> pdb=" O ALA B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 400 through 402 Processing sheet with id= M, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.930A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 141 through 145 removed outlier: 3.633A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 35 through 37 removed outlier: 3.505A pdb=" N GLU C 491 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.308A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 383 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 187 through 189 removed outlier: 3.522A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.752A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 400 through 402 removed outlier: 3.690A pdb=" N LEU C 408 " --> pdb=" O PHE C 401 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.930A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.529A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.535A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 383 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 187 through 189 removed outlier: 3.536A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 400 through 402 Processing sheet with id= Y, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.891A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.555A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= AB, first strand: chain 'E' and resid 187 through 189 removed outlier: 3.592A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.773A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'E' and resid 320 through 323 removed outlier: 7.935A pdb=" N VAL E 323 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 362 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR E 383 " --> pdb=" O ALA E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 409 through 412 Processing sheet with id= AF, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.925A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.536A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AI, first strand: chain 'F' and resid 187 through 189 removed outlier: 7.789A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.764A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'F' and resid 320 through 323 removed outlier: 7.829A pdb=" N VAL F 323 " --> pdb=" O PRO F 360 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE F 362 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR F 383 " --> pdb=" O ALA F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'F' and resid 409 through 412 Processing sheet with id= AM, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.898A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AO, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AP, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.293A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR G 383 " --> pdb=" O ILE G 361 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.291A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.730A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'G' and resid 400 through 402 removed outlier: 3.606A pdb=" N LEU G 408 " --> pdb=" O PHE G 401 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.900A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AV, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.526A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR H 383 " --> pdb=" O ILE H 361 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 187 through 189 removed outlier: 8.090A pdb=" N ALA H 188 " --> pdb=" O LYS H 208 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.778A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'H' and resid 400 through 402 Processing sheet with id= AZ, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.870A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'H' and resid 141 through 145 removed outlier: 3.578A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.51 Time building geometry restraints manager: 37.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 6339 1.06 - 1.25: 27564 1.25 - 1.44: 8324 1.44 - 1.63: 17833 1.63 - 1.82: 324 Bond restraints: 60384 Sorted by residual: bond pdb=" C2' GTP D 601 " pdb=" C3' GTP D 601 " ideal model delta sigma weight residual 1.524 1.226 0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C2' GTP E 601 " pdb=" C3' GTP E 601 " ideal model delta sigma weight residual 1.524 1.227 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C1' GTP D 601 " pdb=" N9 GTP D 601 " ideal model delta sigma weight residual 1.475 1.323 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C1' GTP E 601 " pdb=" N9 GTP E 601 " ideal model delta sigma weight residual 1.475 1.323 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N ILE H 330 " pdb=" H ILE H 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 60379 not shown) Histogram of bond angle deviations from ideal: 93.96 - 102.26: 333 102.26 - 110.57: 60833 110.57 - 118.87: 24477 118.87 - 127.18: 23133 127.18 - 135.48: 368 Bond angle restraints: 109144 Sorted by residual: angle pdb=" PB ATP E 604 " pdb=" O3B ATP E 604 " pdb=" PG ATP E 604 " ideal model delta sigma weight residual 139.87 121.11 18.76 1.00e+00 1.00e+00 3.52e+02 angle pdb=" PB ATP F 604 " pdb=" O3B ATP F 604 " pdb=" PG ATP F 604 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 118.51 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PB ATP D 604 " pdb=" O3B ATP D 604 " pdb=" PG ATP D 604 " ideal model delta sigma weight residual 139.87 121.64 18.23 1.00e+00 1.00e+00 3.32e+02 angle pdb=" PB ATP H 604 " pdb=" O3B ATP H 604 " pdb=" PG ATP H 604 " ideal model delta sigma weight residual 139.87 121.65 18.22 1.00e+00 1.00e+00 3.32e+02 ... (remaining 109139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.80: 26410 29.80 - 59.60: 1689 59.60 - 89.40: 433 89.40 - 119.20: 25 119.20 - 149.00: 43 Dihedral angle restraints: 28600 sinusoidal: 16352 harmonic: 12248 Sorted by residual: dihedral pdb=" C8 GTP E 601 " pdb=" C1' GTP E 601 " pdb=" N9 GTP E 601 " pdb=" O4' GTP E 601 " ideal model delta sinusoidal sigma weight residual 104.59 -106.40 -149.00 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C8 GTP D 601 " pdb=" C1' GTP D 601 " pdb=" N9 GTP D 601 " pdb=" O4' GTP D 601 " ideal model delta sinusoidal sigma weight residual 104.59 -106.43 -148.97 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C4' GTP E 601 " pdb=" C5' GTP E 601 " pdb=" O5' GTP E 601 " pdb=" PA GTP E 601 " ideal model delta sinusoidal sigma weight residual 260.87 112.11 148.76 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 28597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3596 0.102 - 0.205: 1075 0.205 - 0.307: 168 0.307 - 0.409: 16 0.409 - 0.512: 1 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA LYS F 205 " pdb=" N LYS F 205 " pdb=" C LYS F 205 " pdb=" CB LYS F 205 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA THR H 172 " pdb=" N THR H 172 " pdb=" C THR H 172 " pdb=" CB THR H 172 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA THR G 172 " pdb=" N THR G 172 " pdb=" C THR G 172 " pdb=" CB THR G 172 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 4853 not shown) Planarity restraints: 8840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IMP A 603 " -0.335 2.00e-02 2.50e+03 1.55e-01 6.00e+02 pdb=" C2 IMP A 603 " 0.081 2.00e-02 2.50e+03 pdb=" C4 IMP A 603 " 0.136 2.00e-02 2.50e+03 pdb=" C5 IMP A 603 " -0.004 2.00e-02 2.50e+03 pdb=" C6 IMP A 603 " -0.193 2.00e-02 2.50e+03 pdb=" C8 IMP A 603 " 0.143 2.00e-02 2.50e+03 pdb=" N1 IMP A 603 " -0.105 2.00e-02 2.50e+03 pdb=" N3 IMP A 603 " 0.140 2.00e-02 2.50e+03 pdb=" N7 IMP A 603 " 0.019 2.00e-02 2.50e+03 pdb=" N9 IMP A 603 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 224 " 0.226 9.50e-02 1.11e+02 1.31e-01 2.65e+02 pdb=" NE ARG G 224 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG G 224 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG G 224 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG G 224 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG G 224 " -0.092 2.00e-02 2.50e+03 pdb="HH12 ARG G 224 " 0.232 2.00e-02 2.50e+03 pdb="HH21 ARG G 224 " 0.107 2.00e-02 2.50e+03 pdb="HH22 ARG G 224 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP F 604 " -0.212 2.00e-02 2.50e+03 8.92e-02 2.19e+02 pdb=" C2 ATP F 604 " 0.039 2.00e-02 2.50e+03 pdb=" C4 ATP F 604 " 0.074 2.00e-02 2.50e+03 pdb=" C5 ATP F 604 " 0.053 2.00e-02 2.50e+03 pdb=" C6 ATP F 604 " -0.022 2.00e-02 2.50e+03 pdb=" C8 ATP F 604 " 0.059 2.00e-02 2.50e+03 pdb=" N1 ATP F 604 " -0.030 2.00e-02 2.50e+03 pdb=" N3 ATP F 604 " 0.071 2.00e-02 2.50e+03 pdb=" N6 ATP F 604 " -0.134 2.00e-02 2.50e+03 pdb=" N7 ATP F 604 " 0.054 2.00e-02 2.50e+03 pdb=" N9 ATP F 604 " 0.047 2.00e-02 2.50e+03 ... (remaining 8837 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 2801 2.12 - 2.74: 96210 2.74 - 3.36: 172024 3.36 - 3.98: 228959 3.98 - 4.60: 347052 Nonbonded interactions: 847046 Sorted by model distance: nonbonded pdb="HD21 LEU A 38 " pdb=" HD3 ARG D 341 " model vdw 1.502 2.440 nonbonded pdb=" HD3 ARG C 341 " pdb="HD21 LEU D 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG B 341 " pdb="HD21 LEU C 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG A 341 " pdb="HD21 LEU B 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG G 341 " pdb="HD21 LEU H 38 " model vdw 1.507 2.440 ... (remaining 847041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.670 Extract box with map and model: 8.730 Check model and map are aligned: 0.840 Set scattering table: 0.540 Process input model: 138.600 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.298 30840 Z= 0.871 Angle : 1.979 18.755 41952 Z= 1.240 Chirality : 0.094 0.512 4856 Planarity : 0.013 0.155 5160 Dihedral : 19.503 149.003 11864 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.95 % Favored : 92.39 % Rotamer: Outliers : 2.74 % Allowed : 5.29 % Favored : 91.96 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3800 helix: -1.72 (0.13), residues: 1256 sheet: -1.36 (0.23), residues: 456 loop : -0.94 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 125 PHE 0.046 0.009 PHE A 456 TYR 0.109 0.015 TYR B 32 ARG 0.009 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1096 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8461 (tp30) cc_final: 0.8084 (tp30) REVERT: A 129 ASP cc_start: 0.8555 (t0) cc_final: 0.8336 (t0) REVERT: A 135 MET cc_start: 0.7846 (ttp) cc_final: 0.7644 (tmm) REVERT: A 179 MET cc_start: 0.8501 (pp-130) cc_final: 0.8101 (pp-130) REVERT: A 204 SER cc_start: 0.8667 (t) cc_final: 0.8386 (t) REVERT: A 241 GLN cc_start: 0.8047 (mp10) cc_final: 0.7404 (mp10) REVERT: A 274 ASP cc_start: 0.8812 (t0) cc_final: 0.8609 (t0) REVERT: A 286 MET cc_start: 0.8864 (tpt) cc_final: 0.8273 (tpt) REVERT: A 330 ILE cc_start: 0.7885 (tp) cc_final: 0.7586 (tp) REVERT: A 385 MET cc_start: 0.8661 (ttm) cc_final: 0.8406 (ttm) REVERT: A 483 MET cc_start: 0.7658 (tpt) cc_final: 0.7236 (tpt) REVERT: B 78 MET cc_start: 0.8902 (ttm) cc_final: 0.8543 (tpp) REVERT: B 135 MET cc_start: 0.7680 (ttp) cc_final: 0.7450 (tmm) REVERT: B 140 SER cc_start: 0.9089 (t) cc_final: 0.8877 (t) REVERT: B 274 ASP cc_start: 0.8773 (t0) cc_final: 0.8470 (t0) REVERT: B 385 MET cc_start: 0.8757 (ttm) cc_final: 0.8306 (ttm) REVERT: B 483 MET cc_start: 0.7596 (tpt) cc_final: 0.7192 (tpt) REVERT: C 129 ASP cc_start: 0.8162 (t0) cc_final: 0.7869 (t0) REVERT: C 204 SER cc_start: 0.8761 (t) cc_final: 0.8554 (t) REVERT: C 205 LYS cc_start: 0.9198 (ptpp) cc_final: 0.8909 (pttm) REVERT: C 241 GLN cc_start: 0.8058 (mp10) cc_final: 0.7373 (mp10) REVERT: C 274 ASP cc_start: 0.8831 (t0) cc_final: 0.8532 (t0) REVERT: C 284 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (tt) REVERT: C 286 MET cc_start: 0.8887 (tpt) cc_final: 0.8241 (tpt) REVERT: C 466 HIS cc_start: 0.7897 (t-90) cc_final: 0.7656 (t-170) REVERT: C 483 MET cc_start: 0.7659 (tpt) cc_final: 0.7276 (tpt) REVERT: D 32 TYR cc_start: 0.9193 (m-80) cc_final: 0.8227 (m-80) REVERT: D 129 ASP cc_start: 0.8319 (t0) cc_final: 0.8066 (t0) REVERT: D 178 VAL cc_start: 0.8778 (m) cc_final: 0.8564 (m) REVERT: D 215 CYS cc_start: 0.7515 (t) cc_final: 0.7233 (t) REVERT: D 385 MET cc_start: 0.8671 (ttm) cc_final: 0.8061 (ttm) REVERT: D 466 HIS cc_start: 0.7943 (t-90) cc_final: 0.7551 (t-170) REVERT: D 483 MET cc_start: 0.7633 (tpt) cc_final: 0.7235 (tpt) REVERT: D 512 LEU cc_start: 0.5076 (OUTLIER) cc_final: 0.4842 (tp) REVERT: E 42 ILE cc_start: 0.9120 (mt) cc_final: 0.8857 (mt) REVERT: E 129 ASP cc_start: 0.8323 (t0) cc_final: 0.8076 (t0) REVERT: E 135 MET cc_start: 0.7777 (ttp) cc_final: 0.7517 (tmm) REVERT: E 136 ARG cc_start: 0.7166 (ttm-80) cc_final: 0.6901 (ttm-80) REVERT: E 153 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7980 (mtpp) REVERT: E 215 CYS cc_start: 0.7586 (t) cc_final: 0.7259 (t) REVERT: E 241 GLN cc_start: 0.8096 (mp10) cc_final: 0.7449 (mp10) REVERT: E 274 ASP cc_start: 0.8884 (t0) cc_final: 0.8587 (t0) REVERT: E 293 LYS cc_start: 0.8591 (tttt) cc_final: 0.8377 (tppt) REVERT: E 512 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4890 (tp) REVERT: F 58 LYS cc_start: 0.8617 (mttt) cc_final: 0.8399 (mmtp) REVERT: F 129 ASP cc_start: 0.8332 (t0) cc_final: 0.8075 (t0) REVERT: F 135 MET cc_start: 0.7746 (ttp) cc_final: 0.7538 (tmm) REVERT: F 178 VAL cc_start: 0.9029 (m) cc_final: 0.8781 (m) REVERT: F 240 SER cc_start: 0.8531 (p) cc_final: 0.8241 (p) REVERT: F 261 ASP cc_start: 0.7190 (m-30) cc_final: 0.6938 (m-30) REVERT: F 293 LYS cc_start: 0.8594 (tttt) cc_final: 0.8331 (tppt) REVERT: G 178 VAL cc_start: 0.9116 (m) cc_final: 0.8791 (m) REVERT: G 241 GLN cc_start: 0.8214 (mp10) cc_final: 0.7905 (mp10) REVERT: G 284 ILE cc_start: 0.9459 (tt) cc_final: 0.9239 (tt) REVERT: G 286 MET cc_start: 0.8858 (tpt) cc_final: 0.8291 (tpt) REVERT: H 32 TYR cc_start: 0.9198 (m-80) cc_final: 0.8261 (m-80) REVERT: H 48 GLU cc_start: 0.8417 (tp30) cc_final: 0.8062 (tp30) REVERT: H 135 MET cc_start: 0.7798 (ttp) cc_final: 0.7465 (tmm) REVERT: H 178 VAL cc_start: 0.9200 (m) cc_final: 0.8943 (m) REVERT: H 179 MET cc_start: 0.8765 (ppp) cc_final: 0.8504 (ppp) REVERT: H 286 MET cc_start: 0.8911 (tpt) cc_final: 0.8278 (tpt) REVERT: H 293 LYS cc_start: 0.8657 (tttt) cc_final: 0.8432 (tttm) REVERT: H 330 ILE cc_start: 0.8114 (tp) cc_final: 0.7812 (tp) REVERT: H 385 MET cc_start: 0.8634 (ttm) cc_final: 0.8213 (ttm) REVERT: H 466 HIS cc_start: 0.8091 (t-90) cc_final: 0.7840 (t-170) outliers start: 86 outliers final: 32 residues processed: 1160 average time/residue: 0.8010 time to fit residues: 1466.5822 Evaluate side-chains 927 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 892 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.7980 chunk 291 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 300 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 348 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS F 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30840 Z= 0.226 Angle : 0.672 7.659 41952 Z= 0.342 Chirality : 0.045 0.175 4856 Planarity : 0.005 0.055 5160 Dihedral : 19.727 157.928 5162 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 1.91 % Allowed : 12.18 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3800 helix: -0.40 (0.16), residues: 1184 sheet: -1.35 (0.23), residues: 456 loop : -0.83 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 171 PHE 0.015 0.001 PHE A 401 TYR 0.011 0.002 TYR C 282 ARG 0.005 0.001 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 909 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8701 (t0) cc_final: 0.8420 (t0) REVERT: A 135 MET cc_start: 0.7888 (ttp) cc_final: 0.7637 (tmm) REVERT: A 179 MET cc_start: 0.8367 (pp-130) cc_final: 0.7910 (pp-130) REVERT: A 241 GLN cc_start: 0.7895 (mp10) cc_final: 0.7207 (mp10) REVERT: A 274 ASP cc_start: 0.8838 (t0) cc_final: 0.8307 (t0) REVERT: A 286 MET cc_start: 0.8690 (tpt) cc_final: 0.8146 (tpt) REVERT: A 466 HIS cc_start: 0.8116 (t-90) cc_final: 0.7848 (t70) REVERT: A 483 MET cc_start: 0.7597 (tpt) cc_final: 0.7278 (tpt) REVERT: B 135 MET cc_start: 0.7692 (ttp) cc_final: 0.7487 (tmm) REVERT: B 274 ASP cc_start: 0.8976 (t0) cc_final: 0.8776 (t0) REVERT: B 385 MET cc_start: 0.8724 (ttm) cc_final: 0.8491 (ttm) REVERT: B 483 MET cc_start: 0.7573 (tpt) cc_final: 0.7281 (tpt) REVERT: C 171 HIS cc_start: 0.6860 (m90) cc_final: 0.6309 (m90) REVERT: C 179 MET cc_start: 0.8854 (ppp) cc_final: 0.8579 (ppp) REVERT: C 241 GLN cc_start: 0.7899 (mp10) cc_final: 0.7200 (mp10) REVERT: C 286 MET cc_start: 0.8813 (tpt) cc_final: 0.8288 (tpp) REVERT: C 408 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7560 (pp) REVERT: C 483 MET cc_start: 0.7604 (tpt) cc_final: 0.7291 (tpt) REVERT: D 129 ASP cc_start: 0.8610 (t0) cc_final: 0.8308 (t0) REVERT: D 286 MET cc_start: 0.8334 (tpp) cc_final: 0.8072 (tpp) REVERT: D 483 MET cc_start: 0.7545 (tpt) cc_final: 0.7257 (tpt) REVERT: E 129 ASP cc_start: 0.8596 (t0) cc_final: 0.8300 (t0) REVERT: E 136 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.6983 (ttp-110) REVERT: E 153 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7907 (mtpp) REVERT: E 241 GLN cc_start: 0.7923 (mp10) cc_final: 0.7300 (mp10) REVERT: E 408 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7984 (pp) REVERT: E 483 MET cc_start: 0.7581 (tpt) cc_final: 0.7300 (tpt) REVERT: F 129 ASP cc_start: 0.8545 (t0) cc_final: 0.8265 (t0) REVERT: F 136 ARG cc_start: 0.7197 (ttm-80) cc_final: 0.6775 (ttm-80) REVERT: F 175 LEU cc_start: 0.8893 (tp) cc_final: 0.8630 (mp) REVERT: F 178 VAL cc_start: 0.9019 (m) cc_final: 0.8800 (m) REVERT: F 293 LYS cc_start: 0.8597 (tttt) cc_final: 0.8388 (tttp) REVERT: F 408 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7871 (pp) REVERT: F 483 MET cc_start: 0.7577 (tpt) cc_final: 0.7298 (tpt) REVERT: G 103 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8004 (mm-30) REVERT: G 175 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8573 (mp) REVERT: G 199 GLU cc_start: 0.7394 (tp30) cc_final: 0.7058 (tp30) REVERT: G 241 GLN cc_start: 0.8140 (mp10) cc_final: 0.7591 (mp10) REVERT: G 411 TYR cc_start: 0.8858 (t80) cc_final: 0.8653 (t80) REVERT: G 466 HIS cc_start: 0.7868 (t-90) cc_final: 0.7480 (t-90) REVERT: G 483 MET cc_start: 0.7607 (tpt) cc_final: 0.7291 (tpt) REVERT: H 32 TYR cc_start: 0.9200 (m-80) cc_final: 0.8403 (m-80) REVERT: H 135 MET cc_start: 0.7824 (ttp) cc_final: 0.7532 (tmm) REVERT: H 178 VAL cc_start: 0.9137 (m) cc_final: 0.8925 (m) REVERT: H 408 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7596 (pp) REVERT: H 411 TYR cc_start: 0.8828 (t80) cc_final: 0.8624 (t80) REVERT: H 483 MET cc_start: 0.7555 (tpt) cc_final: 0.7261 (tpt) outliers start: 60 outliers final: 44 residues processed: 947 average time/residue: 0.7516 time to fit residues: 1159.0230 Evaluate side-chains 894 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 845 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 349 optimal weight: 0.9980 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 125 HIS C 466 HIS C 498 GLN D 466 HIS ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30840 Z= 0.381 Angle : 0.667 7.721 41952 Z= 0.341 Chirality : 0.046 0.166 4856 Planarity : 0.005 0.059 5160 Dihedral : 18.837 171.684 5149 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.34 % Favored : 93.63 % Rotamer: Outliers : 2.39 % Allowed : 14.03 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3800 helix: -0.66 (0.14), residues: 1272 sheet: -1.51 (0.21), residues: 536 loop : -0.99 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 466 PHE 0.017 0.002 PHE D 401 TYR 0.014 0.002 TYR B 32 ARG 0.005 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 845 time to evaluate : 3.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8795 (t0) cc_final: 0.8569 (t0) REVERT: A 179 MET cc_start: 0.8326 (pp-130) cc_final: 0.7896 (pp-130) REVERT: A 466 HIS cc_start: 0.8192 (t-90) cc_final: 0.7926 (t70) REVERT: C 171 HIS cc_start: 0.7131 (m90) cc_final: 0.6550 (m90) REVERT: C 179 MET cc_start: 0.8899 (ppp) cc_final: 0.8574 (ppp) REVERT: C 241 GLN cc_start: 0.7976 (mp10) cc_final: 0.7335 (mp10) REVERT: C 286 MET cc_start: 0.8760 (tpt) cc_final: 0.8230 (tpp) REVERT: C 408 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7608 (pp) REVERT: D 286 MET cc_start: 0.8395 (tpp) cc_final: 0.8141 (tpp) REVERT: E 153 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7984 (mtpp) REVERT: E 408 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8069 (pp) REVERT: F 241 GLN cc_start: 0.7985 (mp10) cc_final: 0.7587 (mp10) REVERT: F 293 LYS cc_start: 0.8684 (tttt) cc_final: 0.8430 (tttp) REVERT: F 323 VAL cc_start: 0.9769 (p) cc_final: 0.9402 (m) REVERT: F 408 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8079 (pp) REVERT: G 103 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8072 (mm-30) REVERT: G 284 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9065 (tt) REVERT: G 286 MET cc_start: 0.8766 (tpt) cc_final: 0.8542 (tpp) REVERT: H 12 TYR cc_start: 0.8046 (t80) cc_final: 0.7656 (t80) REVERT: H 32 TYR cc_start: 0.9182 (m-80) cc_final: 0.8332 (m-80) REVERT: H 135 MET cc_start: 0.7925 (ttp) cc_final: 0.7509 (tmm) REVERT: H 153 LYS cc_start: 0.8346 (mtpp) cc_final: 0.8130 (mtpp) outliers start: 75 outliers final: 58 residues processed: 885 average time/residue: 0.7712 time to fit residues: 1119.0257 Evaluate side-chains 878 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 816 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 369 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 350 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 332 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 466 HIS D 466 HIS G 241 GLN G 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30840 Z= 0.274 Angle : 0.597 6.810 41952 Z= 0.299 Chirality : 0.044 0.162 4856 Planarity : 0.004 0.058 5160 Dihedral : 18.095 179.126 5135 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 2.42 % Allowed : 15.72 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3800 helix: -0.54 (0.15), residues: 1280 sheet: -1.64 (0.19), residues: 616 loop : -0.90 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 466 PHE 0.012 0.001 PHE A 401 TYR 0.011 0.001 TYR B 32 ARG 0.003 0.000 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 844 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8740 (t0) cc_final: 0.8493 (t0) REVERT: A 179 MET cc_start: 0.8308 (pp-130) cc_final: 0.7877 (pp-130) REVERT: A 464 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8936 (mt) REVERT: A 466 HIS cc_start: 0.8180 (t-90) cc_final: 0.7845 (t-90) REVERT: B 121 LEU cc_start: 0.8488 (mt) cc_final: 0.8233 (mt) REVERT: B 135 MET cc_start: 0.7414 (tmm) cc_final: 0.7051 (tmm) REVERT: B 323 VAL cc_start: 0.9757 (p) cc_final: 0.9406 (m) REVERT: C 171 HIS cc_start: 0.7179 (m90) cc_final: 0.6637 (m90) REVERT: C 241 GLN cc_start: 0.7946 (mp10) cc_final: 0.7312 (mp10) REVERT: C 274 ASP cc_start: 0.8983 (t0) cc_final: 0.8620 (t0) REVERT: C 284 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8994 (mt) REVERT: C 286 MET cc_start: 0.8710 (tpt) cc_final: 0.8212 (tpp) REVERT: C 408 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7594 (pp) REVERT: D 129 ASP cc_start: 0.8480 (t0) cc_final: 0.8084 (t0) REVERT: D 205 LYS cc_start: 0.9189 (ptpp) cc_final: 0.8941 (mtmm) REVERT: D 408 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7573 (pp) REVERT: E 121 LEU cc_start: 0.8511 (mt) cc_final: 0.8177 (mt) REVERT: E 129 ASP cc_start: 0.8395 (t0) cc_final: 0.8142 (t0) REVERT: E 153 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7969 (mtpp) REVERT: E 286 MET cc_start: 0.8256 (tpp) cc_final: 0.7873 (tpp) REVERT: E 323 VAL cc_start: 0.9757 (p) cc_final: 0.9393 (m) REVERT: E 408 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8144 (pp) REVERT: F 241 GLN cc_start: 0.7974 (mp10) cc_final: 0.7597 (mp10) REVERT: F 293 LYS cc_start: 0.8668 (tttt) cc_final: 0.8423 (tttp) REVERT: F 323 VAL cc_start: 0.9757 (p) cc_final: 0.9417 (m) REVERT: F 408 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8093 (pp) REVERT: G 103 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7907 (mm-30) REVERT: H 12 TYR cc_start: 0.7990 (t80) cc_final: 0.7673 (t80) REVERT: H 32 TYR cc_start: 0.9184 (m-80) cc_final: 0.8383 (m-80) REVERT: H 135 MET cc_start: 0.7888 (ttp) cc_final: 0.7622 (tmm) REVERT: H 153 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8116 (mtpp) REVERT: H 323 VAL cc_start: 0.9647 (p) cc_final: 0.9213 (m) REVERT: H 385 MET cc_start: 0.8706 (ttm) cc_final: 0.8232 (ttm) REVERT: H 411 TYR cc_start: 0.9002 (t80) cc_final: 0.8570 (t80) REVERT: H 466 HIS cc_start: 0.8398 (t-90) cc_final: 0.8196 (t70) outliers start: 76 outliers final: 60 residues processed: 887 average time/residue: 0.7425 time to fit residues: 1075.5003 Evaluate side-chains 885 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 819 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 369 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.6144 > 50: distance: 68 - 80: 26.173 distance: 80 - 81: 16.328 distance: 80 - 88: 23.023 distance: 81 - 82: 10.365 distance: 81 - 84: 8.759 distance: 81 - 89: 18.379 distance: 82 - 99: 8.650 distance: 84 - 85: 19.873 distance: 84 - 90: 32.168 distance: 84 - 91: 24.404 distance: 85 - 86: 12.685 distance: 85 - 87: 30.245 distance: 85 - 92: 25.544 distance: 86 - 94: 13.905 distance: 86 - 95: 14.772 distance: 87 - 96: 3.307 distance: 87 - 97: 8.498 distance: 87 - 98: 5.852 distance: 99 - 100: 21.424 distance: 99 - 108: 26.235 distance: 100 - 101: 31.757 distance: 100 - 103: 38.611 distance: 100 - 109: 16.891 distance: 101 - 102: 44.290 distance: 103 - 104: 28.231 distance: 103 - 110: 20.633 distance: 103 - 111: 19.551 distance: 104 - 105: 27.983 distance: 104 - 112: 16.388 distance: 104 - 113: 5.788 distance: 105 - 106: 9.361 distance: 105 - 114: 3.451 distance: 105 - 115: 3.568 distance: 106 - 107: 18.320 distance: 106 - 116: 4.365 distance: 106 - 117: 3.655 distance: 107 - 118: 13.869 distance: 107 - 119: 6.020 distance: 107 - 120: 4.125 distance: 121 - 122: 8.309 distance: 121 - 130: 7.429 distance: 122 - 123: 30.680 distance: 122 - 125: 32.647 distance: 122 - 131: 37.338 distance: 123 - 124: 6.962 distance: 123 - 136: 14.959 distance: 124 - 175: 26.846 distance: 125 - 126: 6.687 distance: 125 - 132: 8.236 distance: 125 - 133: 12.022 distance: 126 - 127: 14.598 distance: 126 - 134: 11.198 distance: 126 - 135: 16.248 distance: 127 - 128: 5.328 distance: 127 - 129: 8.634 distance: 136 - 137: 29.788 distance: 136 - 141: 25.615 distance: 137 - 138: 20.647 distance: 137 - 140: 32.779 distance: 137 - 142: 22.592 distance: 138 - 139: 10.133 distance: 138 - 146: 8.577 distance: 139 - 194: 35.191 distance: 140 - 143: 10.750 distance: 140 - 144: 40.428 distance: 140 - 145: 7.438 distance: 146 - 147: 21.798 distance: 146 - 154: 3.136 distance: 147 - 148: 26.895 distance: 147 - 150: 21.311 distance: 147 - 155: 23.450 distance: 148 - 149: 45.517 distance: 148 - 160: 41.805 distance: 149 - 213: 37.198 distance: 150 - 151: 16.631 distance: 150 - 156: 16.809 distance: 150 - 157: 8.323 distance: 151 - 152: 12.171 distance: 151 - 153: 14.172 distance: 153 - 158: 12.172 distance: 153 - 159: 13.778 distance: 160 - 161: 8.405 distance: 160 - 169: 3.021 distance: 161 - 162: 21.021 distance: 161 - 164: 22.614 distance: 161 - 170: 10.963 distance: 162 - 163: 11.564 distance: 162 - 175: 12.903 distance: 163 - 230: 25.883 distance: 164 - 165: 13.874 distance: 164 - 171: 9.779 distance: 164 - 172: 7.681 distance: 165 - 166: 21.419 distance: 165 - 173: 10.548 distance: 165 - 174: 19.458 distance: 166 - 167: 6.947 distance: 166 - 168: 8.999 distance: 175 - 176: 23.637 distance: 175 - 183: 25.726 distance: 176 - 177: 32.283 distance: 176 - 179: 13.908 distance: 176 - 184: 22.507 distance: 177 - 178: 7.711 distance: 177 - 194: 22.426 distance: 179 - 180: 6.261 distance: 179 - 181: 11.724 distance: 179 - 185: 13.728 distance: 180 - 182: 12.012 distance: 180 - 186: 8.175 distance: 180 - 187: 12.432 distance: 181 - 188: 4.759 distance: 181 - 189: 9.769 distance: 181 - 190: 14.915 distance: 182 - 191: 10.633 distance: 182 - 192: 13.046 distance: 182 - 193: 7.469 distance: 194 - 195: 12.386 distance: 194 - 202: 21.990 distance: 195 - 196: 19.222 distance: 195 - 198: 24.404 distance: 195 - 203: 18.719 distance: 196 - 197: 9.025 distance: 196 - 213: 36.256 distance: 198 - 199: 18.566 distance: 198 - 204: 22.416 distance: 198 - 205: 17.429 distance: 199 - 200: 10.395 distance: 199 - 201: 16.836 distance: 199 - 206: 16.330 distance: 200 - 207: 10.619 distance: 200 - 208: 7.447 distance: 200 - 209: 14.289 distance: 201 - 210: 16.120 distance: 201 - 211: 20.941 distance: 213 - 214: 47.583 distance: 213 - 222: 15.512 distance: 214 - 215: 40.050 distance: 214 - 217: 28.707 distance: 214 - 223: 17.190 distance: 215 - 216: 27.664 distance: 215 - 230: 39.495 distance: 217 - 218: 38.460 distance: 217 - 224: 21.310 distance: 217 - 225: 32.526 distance: 218 - 219: 12.029 distance: 218 - 226: 18.277 distance: 218 - 227: 17.863 distance: 219 - 220: 9.020 distance: 219 - 221: 20.110 distance: 221 - 228: 11.606 distance: 221 - 229: 8.193 distance: 230 - 231: 39.943 distance: 230 - 241: 33.775 distance: 231 - 232: 15.556 distance: 231 - 234: 30.466 distance: 231 - 242: 11.163 distance: 232 - 233: 15.708 distance: 232 - 254: 21.420 distance: 234 - 235: 10.982 distance: 234 - 243: 29.252 distance: 234 - 244: 17.189 distance: 235 - 236: 9.055 distance: 235 - 245: 11.912 distance: 235 - 246: 16.410 distance: 236 - 237: 5.052 distance: 236 - 247: 4.552 distance: 236 - 248: 6.762 distance: 237 - 238: 12.735 distance: 237 - 249: 17.924 distance: 238 - 239: 3.852 distance: 238 - 240: 5.682 distance: 239 - 250: 6.574 distance: 239 - 251: 6.616 distance: 240 - 252: 4.741 distance: 240 - 253: 7.444